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<div class="title">ArgumentHandler.hpp</div>  </div>
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<a href="_argument_handler_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="preprocessor">#ifndef ARGUMENTHANDLER_HPP</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="preprocessor">#define ARGUMENTHANDLER_HPP</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160; </div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="preprocessor">#include &lt;cstdio&gt;</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="preprocessor">#include &lt;cstdlib&gt;</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160; </div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_exception_handler_8hpp.html">ExceptionHandler.hpp</a>&quot;</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_tree_builder_8hpp.html">TreeBuilder.hpp</a>&quot;</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160; </div>
<div class="line"><a name="l00010"></a><span class="lineno"><a class="line" href="class_argument_handler.html">   10</a></span>&#160;<span class="keyword">class </span><a class="code" href="class_argument_handler.html">ArgumentHandler</a> {</div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00014"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854a">   14</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854a">InputType</a> {</div>
<div class="line"><a name="l00015"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aafe3d262ec86ee31ed3d27ef42b1f235a">   15</a></span>&#160;        <a class="code" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aafe3d262ec86ee31ed3d27ef42b1f235a">alignment</a>, <a class="code" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aa9d20bc1085ccd1932c0ffd1d97a10dc6">distance</a></div>
<div class="line"><a name="l00016"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aa9d20bc1085ccd1932c0ffd1d97a10dc6">   16</a></span>&#160;    };</div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160; </div>
<div class="line"><a name="l00019"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6">   19</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6">OutputType</a> {</div>
<div class="line"><a name="l00020"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6a1af730d3ffbdc6354d6bda2549356cef">   20</a></span>&#160;        <a class="code" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6a1af730d3ffbdc6354d6bda2549356cef">dist</a>, <a class="code" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6ab25e481414af792cbeffe6f6e2f06301">tree</a></div>
<div class="line"><a name="l00021"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6ab25e481414af792cbeffe6f6e2f06301">   21</a></span>&#160;    };</div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160; </div>
<div class="line"><a name="l00024"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">   24</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">AlphabetType</a> {</div>
<div class="line"><a name="l00025"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87af8d1253b6d8eecce0eea5eff86ddc63e">   25</a></span>&#160;        <a class="code" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87af8d1253b6d8eecce0eea5eff86ddc63e">dna</a>, <a class="code" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87abf0a7e58c2a951cb200e05ceed789d48">amino</a>, <span class="keyword">null</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87a340fde3e9bbd6b4f6450c7e10baa63a4">   26</a></span>&#160;    };</div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160; </div>
<div class="line"><a name="l00030"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afd">   30</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afd">CorrectionType</a> {</div>
<div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda3bc78094126089bb7a17ff4a5ef7e60f">   31</a></span>&#160;        <a class="code" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda3bc78094126089bb7a17ff4a5ef7e60f">not_assigned</a>, <a class="code" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda2c1d7a65ead4fefe3d70bfc2f64662e0">none</a>, <a class="code" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda73811e507c334774db6b1ab687639b5f">JukesCantor</a>, <a class="code" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda543fa5f6ad05da7f2efa6cefee5ba8d9">Kimura2</a>, <a class="code" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afdab094fe12b9abab259fbf519b9e3399a3">FastTree</a></div>
<div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afdab094fe12b9abab259fbf519b9e3399a3">   32</a></span>&#160;    };</div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160; </div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;    <a class="code" href="class_argument_handler.html#a2657983b12529181db92512d3a6fc1fa">ArgumentHandler</a>(<span class="keywordtype">char</span> *argv[], <span class="keywordtype">int</span> argc);</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160; </div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="class_argument_handler.html#ad6143cf6a96ca5cc6aeb97f432bc629d">getAbort</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160; </div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    std::string <a class="code" href="class_argument_handler.html#ac6b6ce1eb3d6fee43314823c8c3e9e6c">getMethod</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160; </div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;    std::string <a class="code" href="class_argument_handler.html#ad651123ca891c60ec98111817e38b06a">getInputFile</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160; </div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;    std::string <a class="code" href="class_argument_handler.html#a242123ae240bca20b782c544416e2fc3">getNJTmpDir</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160; </div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;    <a class="code" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854a">InputType</a> <a class="code" href="class_argument_handler.html#a32c069acf9792739ceb10c87edf22ddc">getInputType</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160; </div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;    <a class="code" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6">OutputType</a> <a class="code" href="class_argument_handler.html#ab0837386ce1c1f76280c9917572989dc">getOutputType</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160; </div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;    FILE *<a class="code" href="class_argument_handler.html#a1c8fbd4a0c2b3d4235c3ef8b83fd43b8">getOutputFile</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160; </div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keywordtype">int</span> <a class="code" href="class_argument_handler.html#a56ce7d11969a9efb741fa10fc14deed2">getNumThreads</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160; </div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <a class="code" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">AlphabetType</a> <a class="code" href="class_argument_handler.html#a8b8d3d08a48c31c010aa80095f85e7cf">getAlphabetType</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160; </div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;    <a class="code" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afd">CorrectionType</a> <a class="code" href="class_argument_handler.html#ad2b8028126c07aabb8603c44594ffaa6">getCorrectionType</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160; </div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">bool</span> <a class="code" href="class_argument_handler.html#aed3ea207ece08d71c49613911ac8b711">argumentTest</a>();</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160; </div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="class_argument_handler.html#a817493c9c676890ac210e1384191828c">getUseSSE</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160; </div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    <span class="comment">// TODO: use an enum if there are only a few values</span></div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    std::string method; <span class="comment">// default should be &quot;bin&quot; for small, &quot;cand&quot; for large.</span></div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    std::string njTmpDir;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    std::string inputFile; <span class="comment">//works?</span></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <a class="code" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854a">InputType</a> inputType;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <a class="code" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6">OutputType</a> outputType;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <a class="code" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">AlphabetType</a> alphabetType;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <a class="code" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afd">CorrectionType</a> correctionType;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    FILE *outputFile;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    <span class="keywordtype">int</span> numThreads;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    <span class="keywordtype">bool</span> useSSE;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <span class="keywordtype">bool</span> abort;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;};</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160; </div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;<span class="preprocessor">#endif</span></div>
</div><!-- fragment --></div><!-- contents -->
</div><!-- doc-content -->
<div class="ttc" id="aclass_argument_handler_html"><div class="ttname"><a href="class_argument_handler.html">ArgumentHandler</a></div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:10</div></div>
<div class="ttc" id="aclass_argument_handler_html_ad6143cf6a96ca5cc6aeb97f432bc629d"><div class="ttname"><a href="class_argument_handler.html#ad6143cf6a96ca5cc6aeb97f432bc629d">ArgumentHandler::getAbort</a></div><div class="ttdeci">bool getAbort() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:178</div></div>
<div class="ttc" id="a_exception_handler_8hpp_html"><div class="ttname"><a href="_exception_handler_8hpp.html">ExceptionHandler.hpp</a></div></div>
<div class="ttc" id="aclass_argument_handler_html_ae67a9e8d392b5fcc6f75c8fb7a875afda3bc78094126089bb7a17ff4a5ef7e60f"><div class="ttname"><a href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda3bc78094126089bb7a17ff4a5ef7e60f">ArgumentHandler::not_assigned</a></div><div class="ttdeci">@ not_assigned</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:31</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae693a55bec1ed6005f0976a40a7f854aa9d20bc1085ccd1932c0ffd1d97a10dc6"><div class="ttname"><a href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aa9d20bc1085ccd1932c0ffd1d97a10dc6">ArgumentHandler::distance</a></div><div class="ttdeci">@ distance</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:15</div></div>
<div class="ttc" id="aclass_argument_handler_html_a1c8fbd4a0c2b3d4235c3ef8b83fd43b8"><div class="ttname"><a href="class_argument_handler.html#a1c8fbd4a0c2b3d4235c3ef8b83fd43b8">ArgumentHandler::getOutputFile</a></div><div class="ttdeci">FILE * getOutputFile() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:206</div></div>
<div class="ttc" id="aclass_argument_handler_html_a817493c9c676890ac210e1384191828c"><div class="ttname"><a href="class_argument_handler.html#a817493c9c676890ac210e1384191828c">ArgumentHandler::getUseSSE</a></div><div class="ttdeci">bool getUseSSE() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:222</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae67a9e8d392b5fcc6f75c8fb7a875afda2c1d7a65ead4fefe3d70bfc2f64662e0"><div class="ttname"><a href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda2c1d7a65ead4fefe3d70bfc2f64662e0">ArgumentHandler::none</a></div><div class="ttdeci">@ none</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:31</div></div>
<div class="ttc" id="aclass_argument_handler_html_ad651123ca891c60ec98111817e38b06a"><div class="ttname"><a href="class_argument_handler.html#ad651123ca891c60ec98111817e38b06a">ArgumentHandler::getInputFile</a></div><div class="ttdeci">std::string getInputFile() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:182</div></div>
<div class="ttc" id="aclass_argument_handler_html_ac2a6552abc7c6449b625791aefdf6d87abf0a7e58c2a951cb200e05ceed789d48"><div class="ttname"><a href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87abf0a7e58c2a951cb200e05ceed789d48">ArgumentHandler::amino</a></div><div class="ttdeci">@ amino</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:25</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae260b096d1b4cb57e0539b8d37ca1ce6"><div class="ttname"><a href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6">ArgumentHandler::OutputType</a></div><div class="ttdeci">OutputType</div><div class="ttdoc">The output type can be either a distance matrix or a tree.</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:19</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae67a9e8d392b5fcc6f75c8fb7a875afd"><div class="ttname"><a href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afd">ArgumentHandler::CorrectionType</a></div><div class="ttdeci">CorrectionType</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:30</div></div>
<div class="ttc" id="aclass_argument_handler_html_ac2a6552abc7c6449b625791aefdf6d87af8d1253b6d8eecce0eea5eff86ddc63e"><div class="ttname"><a href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87af8d1253b6d8eecce0eea5eff86ddc63e">ArgumentHandler::dna</a></div><div class="ttdeci">@ dna</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:25</div></div>
<div class="ttc" id="aclass_argument_handler_html_a56ce7d11969a9efb741fa10fc14deed2"><div class="ttname"><a href="class_argument_handler.html#a56ce7d11969a9efb741fa10fc14deed2">ArgumentHandler::getNumThreads</a></div><div class="ttdeci">int getNumThreads() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:194</div></div>
<div class="ttc" id="aclass_argument_handler_html_ad2b8028126c07aabb8603c44594ffaa6"><div class="ttname"><a href="class_argument_handler.html#ad2b8028126c07aabb8603c44594ffaa6">ArgumentHandler::getCorrectionType</a></div><div class="ttdeci">CorrectionType getCorrectionType() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:214</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae693a55bec1ed6005f0976a40a7f854aafe3d262ec86ee31ed3d27ef42b1f235a"><div class="ttname"><a href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aafe3d262ec86ee31ed3d27ef42b1f235a">ArgumentHandler::alignment</a></div><div class="ttdeci">@ alignment</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:15</div></div>
<div class="ttc" id="aclass_argument_handler_html_a2657983b12529181db92512d3a6fc1fa"><div class="ttname"><a href="class_argument_handler.html#a2657983b12529181db92512d3a6fc1fa">ArgumentHandler::ArgumentHandler</a></div><div class="ttdeci">ArgumentHandler(char *argv[], int argc)</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:3</div></div>
<div class="ttc" id="aclass_argument_handler_html_a32c069acf9792739ceb10c87edf22ddc"><div class="ttname"><a href="class_argument_handler.html#a32c069acf9792739ceb10c87edf22ddc">ArgumentHandler::getInputType</a></div><div class="ttdeci">InputType getInputType() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:186</div></div>
<div class="ttc" id="a_tree_builder_8hpp_html"><div class="ttname"><a href="_tree_builder_8hpp.html">TreeBuilder.hpp</a></div></div>
<div class="ttc" id="aclass_argument_handler_html_ac2a6552abc7c6449b625791aefdf6d87"><div class="ttname"><a href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">ArgumentHandler::AlphabetType</a></div><div class="ttdeci">AlphabetType</div><div class="ttdoc">The alphabet to use; either the DNA nucleotides or amino acids.</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:24</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae260b096d1b4cb57e0539b8d37ca1ce6ab25e481414af792cbeffe6f6e2f06301"><div class="ttname"><a href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6ab25e481414af792cbeffe6f6e2f06301">ArgumentHandler::tree</a></div><div class="ttdeci">@ tree</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:20</div></div>
<div class="ttc" id="aclass_argument_handler_html_ac6b6ce1eb3d6fee43314823c8c3e9e6c"><div class="ttname"><a href="class_argument_handler.html#ac6b6ce1eb3d6fee43314823c8c3e9e6c">ArgumentHandler::getMethod</a></div><div class="ttdeci">std::string getMethod() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:190</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae67a9e8d392b5fcc6f75c8fb7a875afda73811e507c334774db6b1ab687639b5f"><div class="ttname"><a href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda73811e507c334774db6b1ab687639b5f">ArgumentHandler::JukesCantor</a></div><div class="ttdeci">@ JukesCantor</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:31</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae260b096d1b4cb57e0539b8d37ca1ce6a1af730d3ffbdc6354d6bda2549356cef"><div class="ttname"><a href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6a1af730d3ffbdc6354d6bda2549356cef">ArgumentHandler::dist</a></div><div class="ttdeci">@ dist</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:20</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae67a9e8d392b5fcc6f75c8fb7a875afda543fa5f6ad05da7f2efa6cefee5ba8d9"><div class="ttname"><a href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda543fa5f6ad05da7f2efa6cefee5ba8d9">ArgumentHandler::Kimura2</a></div><div class="ttdeci">@ Kimura2</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:31</div></div>
<div class="ttc" id="aclass_argument_handler_html_ab0837386ce1c1f76280c9917572989dc"><div class="ttname"><a href="class_argument_handler.html#ab0837386ce1c1f76280c9917572989dc">ArgumentHandler::getOutputType</a></div><div class="ttdeci">OutputType getOutputType() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:202</div></div>
<div class="ttc" id="aclass_argument_handler_html_aed3ea207ece08d71c49613911ac8b711"><div class="ttname"><a href="class_argument_handler.html#aed3ea207ece08d71c49613911ac8b711">ArgumentHandler::argumentTest</a></div><div class="ttdeci">static bool argumentTest()</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:218</div></div>
<div class="ttc" id="aclass_argument_handler_html_a8b8d3d08a48c31c010aa80095f85e7cf"><div class="ttname"><a href="class_argument_handler.html#a8b8d3d08a48c31c010aa80095f85e7cf">ArgumentHandler::getAlphabetType</a></div><div class="ttdeci">AlphabetType getAlphabetType() const</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:210</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae67a9e8d392b5fcc6f75c8fb7a875afdab094fe12b9abab259fbf519b9e3399a3"><div class="ttname"><a href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afdab094fe12b9abab259fbf519b9e3399a3">ArgumentHandler::FastTree</a></div><div class="ttdeci">@ FastTree</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:31</div></div>
<div class="ttc" id="aclass_argument_handler_html_a242123ae240bca20b782c544416e2fc3"><div class="ttname"><a href="class_argument_handler.html#a242123ae240bca20b782c544416e2fc3">ArgumentHandler::getNJTmpDir</a></div><div class="ttdeci">std::string getNJTmpDir() const</div><div class="ttdoc">Get the temporary directory used for the neighbor-joining algorithm.</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.cpp:198</div></div>
<div class="ttc" id="aclass_argument_handler_html_ae693a55bec1ed6005f0976a40a7f854a"><div class="ttname"><a href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854a">ArgumentHandler::InputType</a></div><div class="ttdeci">InputType</div><div class="ttdef"><b>Definition:</b> ArgumentHandler.hpp:14</div></div>
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